| Variant ID: vg1007738365 (JBrowse) | Variation Type: SNP |
| Chromosome: chr10 | Position: 7738365 |
| Reference Allele: T | Alternative Allele: A |
| Primary Allele: T | Secondary Allele: A |
Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.01, others allele: 0.00, population size: 318. )
CACAACTCAAAGTAAAGTACAGTGCACAAACTACCAGGTGCCACCAGATGACTGTCCAGTACCACCAGTGCGTATAAATTCCAAGCGCCTAGCGGCGTCC[T/A]
TGAGTCGAACAAAGCATTTGCAGGTGAATGGGTCACGGAATAGCGCACAAGCAGCATACCACACACTTCCTCCAATTTCATGGCCATCATTTTCCACCAA
TTGGTGGAAAATGATGGCCATGAAATTGGAGGAAGTGTGTGGTATGCTGCTTGTGCGCTATTCCGTGACCCATTCACCTGCAAATGCTTTGTTCGACTCA[A/T]
GGACGCCGCTAGGCGCTTGGAATTTATACGCACTGGTGGTACTGGACAGTCATCTGGTGGCACCTGGTAGTTTGTGCACTGTACTTTACTTTGAGTTGTG
| Populations | Population Size | Frequency of T(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 87.60% | 0.00% | 2.03% | 10.30% | NA |
| All Indica | 2759 | 89.90% | 0.00% | 1.99% | 8.05% | NA |
| All Japonica | 1512 | 80.50% | 0.00% | 2.38% | 17.13% | NA |
| Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica I | 595 | 79.30% | 0.00% | 3.87% | 16.81% | NA |
| Indica II | 465 | 91.20% | 0.00% | 2.80% | 6.02% | NA |
| Indica III | 913 | 96.80% | 0.10% | 0.33% | 2.74% | NA |
| Indica Intermediate | 786 | 89.20% | 0.00% | 2.04% | 8.78% | NA |
| Temperate Japonica | 767 | 82.30% | 0.00% | 1.83% | 15.91% | NA |
| Tropical Japonica | 504 | 81.00% | 0.00% | 3.77% | 15.28% | NA |
| Japonica Intermediate | 241 | 73.90% | 0.00% | 1.24% | 24.90% | NA |
| VI/Aromatic | 96 | 94.80% | 0.00% | 5.21% | 0.00% | NA |
| Intermediate | 90 | 93.30% | 0.00% | 0.00% | 6.67% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1007738365 | T -> A | LOC_Os10g14290.1 | missense_variant ; p.Lys382Met; MODERATE | nonsynonymous_codon ; K382M | Average:6.018; most accessible tissue: Minghui63 young leaf, score: 12.713 | unknown | unknown | DELETERIOUS | 0.02 |
| vg1007738365 | T -> DEL | LOC_Os10g14290.1 | N | frameshift_variant | Average:6.018; most accessible tissue: Minghui63 young leaf, score: 12.713 | N | N | N | N |